Re: [maq-help] SNP filtering and calling

[Heng Li <lh...@gm...>]

Dear Olivier,

Thanks for the feed back. maq-0.6.2 and maq-0.6.1 use different rules  
in filtering SNPs. In maq-0.6.2, the following rules are used to get  
cns.final.snp:

"After mapping and consensus base calling, we filtered the SNPs based on
four rules: [i') discard SNPs in 3bp-flanking regions beside potential
indels;] i) discard SNPs covered by three or fewer reads; ii) discard
SNPs covered by no read with a mapping quality higher than 40; iii) in
any 10bp window, if there are 3 or more SNPs, discard them all; and iv)
discard SNPs with quality smaller than 40."

In some cases, you can reduce the threshold on the quality of SNP  
(rule iv), but the false positive may increase a little. For single- 
end reads, you may also try:

maq.pl SNPfilter -a cns.snp > cns.filtered.snp

This command will invoke an alternative filter which is with similar  
aim but slightly different from rule ii).

As for the last column in *.snp, you can ignore them. Even I do not  
use them any longer. Maybe I should remove that column some day.

Hope this helps.

Cheers,

Heng


On 27 Nov 2007, at 22:20, Olivier Harismendy wrote:

> Hi,
>
> I have question about the cns.final.snp output file from maq.pl  
> easyrun.
>
> What are the filters applied to the SNPs (depth/repeats/quality) ?  
> Is there a way to play with the parameters ?
>
> In the output, the last column (quality difference between strong  
> and weak allele) doesn't make sense to me as the values go from  
> -124 to 124. Can you explain a little ?
>
> thanks for your answer.
>
> Olivier
>
>
>
>
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